AMBER Archive (2008)

Subject: Re: AMBER: Which is best temperature controlling method

From: sudipta sinha (sudipta.mml_at_gmail.com)
Date: Wed May 28 2008 - 01:43:32 CDT

Hi All,

I am wondering whether the Nose-Hoover chain thermostating or the 'extended
phase space' approach implemented in AMBER.

Although computationally expensive, but this is possibly the best
non-Hamiltonian MD scheme capable of generating proper NVT or NPT ensemble
distribution.

regards
sudipta

On Wed, May 28, 2008 at 11:04 AM, Reena ..... <ren.saini_at_gmail.com> wrote:

> hello,
>
> I am too new to amber. Just read your query and answer to it by Dr. Case.
> I didnt understand the last part of the answer
> " You are right to be worried about the random part: be sure to select a
> new
> random number seed for each restart."
> New random no. seed for each restart????? what does this mean?
> Please elaborate more on it.
>
> regards
>
> A curious student.....:)
>
>
> On Wed, May 28, 2008 at 10:29 AM, David A. Case <case_at_scripps.edu> wrote:
>
>> On Tue, May 27, 2008, sudipta sinha wrote:
>> >
>> > I am new in the AMBER world and I am using AMBER9. I want to do
>> > NVT, NPT simulation of a biomolecule in explicit water and I am also
>> > interested to calculate some equilibrium dynamical properties through
>> > various types of correlation function. My problem is choosing the best
>> > algorithm of temperature controlling for such type of analysis. There
>> are
>> > three different methods included in AMBER9 for temperature controlling.
>> > 1)NTT=1 weak coupling algorithm (basically a temperature scaling
>> algorithm.
>> > so it is not a good algorithm)
>> > 2)NTT=2 Anderson method (A random part is included)
>> > 3) NTT=3 Langevin dynamics (Here also a random part is included)
>> > I am worried about the random part. Is the random part deviate the
>> actual
>> > dynamics? Among them which is the best algorithm for calculating such
>> type
>> > of equilibrium dynamical quantities? Could anyone suggest me?
>>
>> The best (really only) way to calculate time correlation functions is to
>> equilibrate with the thermostat of your choice (usually ntt=3) and then
>> run
>> NVE simulations. With explicit water, the difference between NVE and NVT
>> on
>> an equilibrated simualation is quite small.
>>
>> You are right to be worried about the random part: be sure to select a new
>> random number seed for each restart.
>>
>> ...dac
>>
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>
>

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